Clark, who joined the MOD in 2002 as comms adviser and chief speech-writer to the secretary of state, will take the title director of news.
He will deal with affairs around the British military's operations in Iraq and Afghanistan, as well as wider reputational issues, overseeing a core comms team of 24 and a 100-strong media operation in Uxbridge.
"There is a lot of aggressive reporting on the way we operate in Iraq, which brings internal and external comms challenges. It does not help soldiers if they think their reputation is being battered [at home]," he said.
Clark added the armed services needed to preserve their reputation in the face of real-time reporting from conflict zones by in-the-field journalists armed with kit such as satellite phones.
Other issues facing the MoD include complaints about low flying in training sessions, and concerns over the environmental impact of military activity. In January some environmentalists suggested the Navy's use of sonar in the North Sea was to blame for a whale becoming disoriented in the Thames.
Reporting to MoD comms director John Pitt-Brook, Clark will act as press secretary to John Reid, accompanying the Secretary of State for Defence on official visits.
He replaces Simon Wren, who left the post after just nine months to become head of news at the Home Office. Before Wren, the post was held by Pam Teare, a witness in the Hutton inquiry and author of the Q&A briefing that led to the naming of Dr David Kelly.
The MoD is not seeking to fill Clark's former role.
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